Don't autocrop video when having different dimensions of videos
First set your render settings Resolution to X:1000 px and Y:1000 px. In Video Sequence Editor right click on the name of the video that you are editing with the ending .001 (or similar). Open the options window with N and select Crop option and crop away the top, bottom, left and right to get the size that you need. To constantly see what you are doing the option at the bottom Use Backdrop is also good to be turned on.